Haggis, whose 2005 film Crash won two Oscars, said that he could no longer remain part "of an organisation where gay-bashing was tolerated".

In a lengthy resignation letter leaked to the press, Haggis attacked the church's support for Proposition 8, which banned same-sex marriage in California.

The letter was addressed to the church's official spokesman Tommy Davis, accusing him of failing to act on promises to distance the organisation from homophobic statements made by its San Diego branch during debates over Proposition 8 last year.

"I called and wrote and implored you, as the official spokesman of the church, to condemn their actions," he wrote. "You promised action. Ten months passed. No action."

He added: "The church’s refusal to denounce the actions of these bigots, hypocrites and homophobes is cowardly. I can think of no other word. Silence is consent, Tommy. I refuse to consent."

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Haggis, a Canadian-born filmmaker who wrote Clint Eastwood's Million Dollar Baby before writing and directing the acclaimed Crash about racial tension in Los Angeles, also claimed that his wife suffered "terrible personal pain" after cutting ties with her parents – former church members – last year.

The director went on to lament his own failure to challenge the church hierarchy earlier in his membership.

"The great majority of Scientologists I know are good people who are genuinely interested in improving conditions on this planet and helping others," he wrote.

"I have to believe that if they knew what I now know, they too would be horrified. But I know how easy it was for me to defend our organisation and dismiss our critics, without ever truly looking at what was being said; I did it for thirty-five years."

Haggis's resignation caps a difficult few days for the Church of Scientology, which was founded by the science fiction writer L Ron Hubbard in 1953.

Mr Davis, the Scientology spokesman to whom the letter was addressed, vehemently denied that the church was homphobic

"Paul had a disagreement with the church that went beyond anything to do with the church," he told the Telegraph. "He wanted the church to take an active political stance and that is something we never do."

He added: "We are a minority ourselves and we support civil rights for everyone."

Mr Davis said he was very disappointed that Haggis's letter - which he said was written three or four months ago - had been made public. He also denied the film-maker's claims that his wife had been forced to "disconnect" from her parents, who had left the church several years ago.

"The church has no policy of disconnection, that is completely untrue. It just does not happen," he said.

On Saturday Mr Davis was shown walking out of an interview with Martin Bashir on the ABC network's Nightline programme after being asked whether the church believed that the earth was populated by an alien lord called Xenu 75 million years ago.